This study is part of a 15-year project to develop less invasive methods to diagnose pneumocystis pneumonia and to predict responses to therapy. Oral washes, induced sputum, and bronchalveolar lavage have been collected from patients with immunosuppressive diseases and respiratory syndromes. During this trial resulting studies have moved the field from a focus on tissue to a focus on respiratory secretions, especially secretions that can be obtained non-invasively. Oral washes have been collected prospectively from patients at San Francisco General Hospital who have HIV infection and possible pneumocystis pneumonia. Quantitative PCR had a high sensitivity and high specificity for identifying patients with pneumocystis penumonia, especially if a cut-off of 50 copies/uL were used. The initial phase of the study is completed. Technical refinements are being assessed and new patient populations are being assessed. These techniques are being applied to new specimens collected at UCSF and NIH. The goal of current studies is to validate prior techniques and diagnostic criteria, and attempt to commercialize the assay. A large patient series is currently being evaluated prospectively.